changeset 5:a9f4a217dcd6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 28506788978bf5f0ce31dca09b7ca3d6d4900edb"
author iuc
date Fri, 02 Jul 2021 20:12:35 +0000
parents f732237754fc
children 34e55239e68b
files macros.xml tools.yml topics/metagenomics/metadata.yaml topics/metagenomics/tutorials/dada2/tutorial.bib topics/metagenomics/tutorials/dada2/tutorial.md topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga
diffstat 6 files changed, 1 insertions(+), 1504 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Feb 01 20:16:57 2021 +0000
+++ b/macros.xml	Fri Jul 02 20:12:35 2021 +0000
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@DADA2_VERSION@">1.18</token>
+    <token name="@DADA2_VERSION@">1.20</token>
     <token name="@WRAPPER_VERSION@">0</token>
 
     <xml name="version_command">
--- a/tools.yml	Mon Feb 01 20:16:57 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-install_tool_dependencies: True
-install_repository_dependencies: True
-install_resolver_dependencies: True
-
-tools: []
--- a/topics/metagenomics/metadata.yaml	Mon Feb 01 20:16:57 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
----
-name: "metagenomics"
-type: "use"
-title: "Metagenomics"
-summary: "Metagenomics is a discipline that enables the genomic study of uncultured microorganisms"
-edam_ontology: "topic_3174"
-docker_image: "quay.io/galaxy/metagenomics-training"
-
-requirements:
-  -
-    type: "internal"
-    topic_name: introduction
-
-maintainers:
-  - bebatut
-  - shiltemann
-
-references:
-  -
-    authors: "Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD."
-    title: "Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology"
-    link: "http://www.schlosslab.org/assets/pdf/2013_kozich.pdf"
-    summary: ""
-  -
-    authors: "Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra"
-    title: "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences."
-    link: "https://www.ncbi.nlm.nih.gov/pubmed/25118885"
-    summary: ""
--- a/topics/metagenomics/tutorials/dada2/tutorial.bib	Mon Feb 01 20:16:57 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-
-# This is the bibliography file for your tutorial.
-#
-# To add bibliography (bibtex) entries here, follow these steps:
-#  1) Find the DOI for the article you want to cite
-#  2) Go to https://doi2bib.org and fill in the DOI
-#  3) Copy the resulting bibtex entry into this file
-#
-# To cite the example below, in your tutorial.md file
-# use {% Batut2018 %}
-
-@article{Batut2018,
-  doi = {10.1016/j.cels.2018.05.012},
-  url = {https://doi.org/10.1016/j.cels.2018.05.012},
-  year = {2018},
-  month = jun,
-  publisher = {Elsevier {BV}},
-  volume = {6},
-  number = {6},
-  pages = {752--758.e1},
-  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
-           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
-           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
-           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
-           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
-           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
-           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
-  title = {Community-Driven Data Analysis Training for Biology},
-  journal = {Cell Systems}
-}
\ No newline at end of file
--- a/topics/metagenomics/tutorials/dada2/tutorial.md	Mon Feb 01 20:16:57 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,642 +0,0 @@
----
-layout: tutorial_hands_on
-
-title: 16S Microbial Analysis with mothur (extended)
-zenodo_link: https://doi.org/10.5281/zenodo.800651
-questions:
-- What is the effect of normal variation in the gut microbiome on host health?
-objectives:
-- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
-- Using a mock community to assess the error rate of your sequencing experiment
-- Visualize sample diversity using Krona and Phinch
-time_estimation: ''
-key_points:
-- 16S rRNA gene sequencing analysis results depend on the many algorithms used and
-  their settings
-- Quality control and cleaning of your data is a crucial step in order to obtain optimal
-  results
-- Adding a mock community to serve as a control sample can help you asses the error
-  rate of your experimental setup
-- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations
-contributors:
-- shiltemann
-- bebatut
-- tnabtaf
-
----
-
-
-# Introduction
-{:.no_toc}
-
-<!-- This is a comment. -->
-
-General introduction about the topic and then an introduction of the
-tutorial (the questions and the objectives). It is nice also to have a
-scheme to sum up the pipeline used during the tutorial. The idea is to
-give to trainees insight into the content of the tutorial and the (theoretical
-and technical) key concepts they will learn.
-
-You may want to cite some publications; this can be done by adding citations to the
-bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations
-must be in bibtex format. If you have the DOI for the paper you wish to cite, you can
-get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org).
-
-With the example you will find in the `tutorial.bib` file, you can add a citation to
-this article here in your tutorial like this:
-{% raw %} `{% cite Batut2018 %}`{% endraw %}.
-This will be rendered like this: {% cite Batut2018 %}, and links to a
-[bibliography section](#bibliography) which will automatically be created at the end of the
-tutorial.
-
-
-**Please follow our
-[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)**
-
-> ### Agenda
->
-> In this tutorial, we will cover:
->
-> 1. TOC
-> {:toc}
->
-{: .agenda}
-
-# Title for your first section
-
-Give some background about what the trainees will be doing in the section.
-Remember that many people reading your materials will likely be novices,
-so make sure to explain all the relevant concepts.
-
-## Title for a subsection
-Section and subsection titles will be displayed in the tutorial index on the left side of
-the page, so try to make them informative and concise!
-
-# Hands-on Sections
-Below are a series of hand-on boxes, one for each tool in your workflow file.
-Often you may wish to combine several boxes into one or make other adjustments such
-as breaking the tutorial into sections, we encourage you to make such changes as you
-see fit, this is just a starting point :)
-
-Anywhere you find the word "***TODO***", there is something that needs to be changed
-depending on the specifics of your tutorial.
-
-have fun!
-
-## Get data
-
-> ### {% icon hands_on %} Hands-on: Data upload
->
-> 1. Create a new history for this tutorial
-> 2. Import the files from [Zenodo]() or from the shared data library
->
->    ```
->    
->    ```
->    ***TODO***: *Add the files by the ones on Zenodo here (if not added)*
->
->    ***TODO***: *Remove the useless files (if added)*
->
->    {% include snippets/import_via_link.md %}
->    {% include snippets/import_from_data_library.md %}
->
-> 3. Rename the datasets
-> 4. Check that the datatype
->
->    {% include snippets/change_datatype.md datatype="datatypes" %}
->
-> 5. Add to each database a tag corresponding to ...
->
->    {% include snippets/add_tag.md %}
->
-{: .hands_on}
-
-# Title of the section usually corresponding to a big step in the analysis
-
-It comes first a description of the step: some background and some theory.
-Some image can be added there to support the theory explanation:
-
-![Alternative text](../../images/image_name "Legend of the image")
-
-The idea is to keep the theory description before quite simple to focus more on the practical part.
-
-***TODO***: *Consider adding a detail box to expand the theory*
-
-> ### {% icon details %} More details about the theory
->
-> But to describe more details, it is possible to use the detail boxes which are expandable
->
-{: .details}
-
-A big step can have several subsections or sub steps:
-
-
-## Sub-step with **dada2_plotComplexity**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_plotQualityProfile**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_filterAndTrim**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_filterAndTrim** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_plotComplexity**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_plotQualityProfile**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **Unzip Collection**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **Unzip Collection** {% icon tool %} with the following parameters:
->    - {% icon param-file %} *"Input Paired Dataset"*: `paired_output` (output of **dada2_filterAndTrim** {% icon tool %})
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_learnErrors**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_learnErrors** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_learnErrors**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_learnErrors** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_dada**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_dada** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_dada**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_dada** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_mergePairs**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_mergePairs** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_makeSequenceTable**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_removeBimeraDenovo**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_seqCounts**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_seqCounts** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-## Sub-step with **dada2_assignTaxonomyAddspecies**
-
-> ### {% icon hands_on %} Hands-on: Task description
->
-> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters:
->
->    ***TODO***: *Check parameter descriptions*
->
->    ***TODO***: *Consider adding a comment or tip box*
->
->    > ### {% icon comment %} Comment
->    >
->    > A comment about the tool or something else. This box can also be in the main text
->    {: .comment}
->
-{: .hands_on}
-
-***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
-
-> ### {% icon question %} Questions
->
-> 1. Question1?
-> 2. Question2?
->
-> > ### {% icon solution %} Solution
-> >
-> > 1. Answer for question1
-> > 2. Answer for question2
-> >
-> {: .solution}
->
-{: .question}
-
-
-## Re-arrange
-
-To create the template, each step of the workflow had its own subsection.
-
-***TODO***: *Re-arrange the generated subsections into sections or other subsections.
-Consider merging some hands-on boxes to have a meaningful flow of the analyses*
-
-# Conclusion
-{:.no_toc}
-
-Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the
-pipeline used.
\ No newline at end of file
--- a/topics/metagenomics/tutorials/dada2/workflows/main_workflow.ga	Mon Feb 01 20:16:57 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,798 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "dada2 for paired data (imported from uploaded file)", 
-    "steps": {
-        "0": {
-            "annotation": "", 
-            "content_id": null, 
-            "errors": null, 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset Collection"
-                }
-            ], 
-            "label": null, 
-            "name": "Input dataset collection", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 613
-            }, 
-            "tool_id": null, 
-            "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"Input Dataset Collection\"}", 
-            "tool_version": null, 
-            "type": "data_collection_input", 
-            "uuid": "b1f16224-49d2-4b7a-a37d-3d93c54f679f", 
-            "workflow_outputs": []
-        }, 
-        "1": {
-            "annotation": "", 
-            "content_id": "dada2_plotComplexity", 
-            "errors": null, 
-            "id": 1, 
-            "input_connections": {
-                "batch_cond|paired_cond|reads": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "dada2: plotComplexity", 
-            "outputs": [
-                {
-                    "name": "output_fwd", 
-                    "type": "pdf"
-                }, 
-                {
-                    "name": "output_rev", 
-                    "type": "pdf"
-                }
-            ], 
-            "position": {
-                "left": 499, 
-                "top": 178.5
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